Welcome to the PRISM documentation! This directory contains comprehensive guides for using the PRISM (Profiling of RNA In-situ through Single-round iMaging) post-stitching pipeline.
- Quick Start - Get up and running with PRISM quickly
- Installation Guide - Complete installation instructions, optional extras, and GPU notes
- Detailed Usage Guide - Comprehensive, step-by-step workflow documentation
- Configuration Guide - Parameter configuration for readout, gene calling, and segmentation
- Data Architecture - Data structure and directory layout requirements
- Changelog - Project change history
- Start with Quick Start to understand the basic workflow
- Follow Installation Guide to set up your environment
- Use Detailed Usage Guide for step-by-step instructions
- Check Configuration Guide for parameter tuning
- Use Detailed Usage Guide for specific workflow steps
- Spot Detection / Readout: Detect RNA spots from stitched images (default: spotiflow; fallback: tophat-based traditional methods) and read out per-channel intensities
- Gene Calling: Assign genes via Gaussian Mixture Models (GMM / codebook-GMM; PoSTcode available as an experimental option)
- Cell Segmentation: Segment nuclei from DAPI and build cell-by-gene expression matrices
Upstream steps (probe design, image acquisition / stitching) are handled by the companion probe_designer and spatial_img_core packages. spatial_img_core is not yet public — request access at huanglab111@gmail.com.
See Data Sources in the main README for the Zenodo sample datasets and raw-image downloads.
- Probe Design: probe_designer
- 3D Segmentation: StarDist
- 3D Spot Detection: AIRLOCALIZE (invoked through
spatial_img_core)
For questions or support, contact us at: huanglab111@gmail.com
If you use PRISM in your research, please cite: